Variant report

Variant	rs1242488
Chromosome Location	chr17:17347995-17347996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17347836..17349791-chr17:17356884..17358605,2	MCF-7	breast:
2	chr17:17347895..17349442-chr17:17385421..17387724,2	MCF-7	breast:
3	chr17:17260627..17264124-chr17:17347628..17351557,3	MCF-7	breast:
4	chr17:17341170..17345071-chr17:17347034..17351413,6	MCF-7	breast:
5	chr17:17345336..17348353-chr17:17348575..17352300,3	K562	blood:
6	chr17:17347625..17349777-chr17:17725439..17727969,2	MCF-7	breast:
7	chr17:17345875..17348341-chr17:17739755..17742747,2	MCF-7	breast:
8	chr17:17337262..17338945-chr17:17347016..17349151,2	MCF-7	breast:
9	chr17:17265082..17270324-chr17:17346925..17351276,6	MCF-7	breast:
10	chr17:17347145..17349329-chr17:17355004..17356599,2	MCF-7	breast:
11	chr17:17346012..17348708-chr17:17349032..17351296,2	MCF-7	breast:
12	chr17:17344282..17356772-chr17:17394630..17405312,31	MCF-7	breast:
13	chr17:17342531..17346072-chr17:17347773..17351460,6	MCF-7	breast:
14	chr17:17347048..17349813-chr17:17378788..17383911,5	MCF-7	breast:
15	chr17:17335195..17342131-chr17:17347291..17351486,7	MCF-7	breast:
16	chr17:17346876..17348557-chr17:17721789..17724493,2	MCF-7	breast:
17	chr17:17290573..17292126-chr17:17346940..17348569,2	MCF-7	breast:
18	chr17:17257302..17260550-chr17:17346867..17350783,4	MCF-7	breast:
19	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
20	chr17:17303519..17305319-chr17:17347425..17348955,2	MCF-7	breast:
21	chr17:17347016..17350522-chr17:17380134..17385375,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141026	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1242477	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242478	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242479	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242480	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242481	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242482	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242484	0.80[GIH][hapmap]
rs1242485	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242486	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242487	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1242509	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16961730	0.83[CEU][hapmap]
rs2694924	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058849	chr17:17308009-17348548	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1058804	chr17:17308984-17348548	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv574523	chr17:17310886-17347995	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1056137	chr17:17311017-17348939	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv543235	chr17:17311017-17348939	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17330200-17350000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:17335400-17348800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:17344000-17348400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr17:17344000-17348600	Weak transcription	Gastric	stomach
5	chr17:17344000-17348800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:17344000-17348800	Weak transcription	Fetal Heart	heart
7	chr17:17344000-17349000	Weak transcription	Right Atrium	heart
8	chr17:17344000-17350000	Weak transcription	Dnd41	blood
9	chr17:17344200-17348400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:17344200-17348600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr17:17344600-17348600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:17344800-17348400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:17344800-17348600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:17344800-17348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:17344800-17348600	Weak transcription	Fetal Muscle Leg	muscle
16	chr17:17344800-17348800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:17344800-17348800	Weak transcription	NHDF-Ad	bronchial
18	chr17:17344800-17349000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:17344800-17349000	Weak transcription	Left Ventricle	heart
20	chr17:17344800-17353400	Weak transcription	Brain Germinal Matrix	brain
21	chr17:17345000-17348400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr17:17346200-17348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:17346400-17348600	Enhancers	A549	lung
24	chr17:17346800-17352200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:17347000-17348200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:17347200-17348400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:17347200-17350000	Weak transcription	Thymus	Thymus
28	chr17:17347400-17348800	Weak transcription	Liver	Liver
29	chr17:17347600-17348200	Weak transcription	Spleen	Spleen
30	chr17:17347600-17348200	Enhancers	Hela-S3	cervix
31	chr17:17347600-17348800	Weak transcription	Lung	lung
32	chr17:17347800-17348200	Weak transcription	Adipose Nuclei	Adipose
33	chr17:17347800-17348200	Weak transcription	Fetal Thymus	thymus
34	chr17:17347800-17348200	Weak transcription	Pancreas	Pancrea
35	chr17:17347800-17348200	Enhancers	HepG2	liver
36	chr17:17347800-17348200	Weak transcription	HUVEC	blood vessel

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